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Yorodumi- PDB-8c32: Dark state 2.2 Angstrom crystal structure of cobalamin binding do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c32 | ||||||
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Title | Dark state 2.2 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under anaerobic condition | ||||||
Components | Probable transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / CarH / cobalamin / light-activated / transcription regulator | ||||||
Function / homology | Function and homology information cobalamin binding / DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Poddar, H. / Leys, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Redox driven B 12 -ligand switch drives CarH photoresponse. Authors: Poddar, H. / Rios-Santacruz, R. / Heyes, D.J. / Shanmugam, M. / Brookfield, A. / Johannissen, L.O. / Levy, C.W. / Jeffreys, L.N. / Zhang, S. / Sakuma, M. / Colletier, J.P. / Hay, S. / ...Authors: Poddar, H. / Rios-Santacruz, R. / Heyes, D.J. / Shanmugam, M. / Brookfield, A. / Johannissen, L.O. / Levy, C.W. / Jeffreys, L.N. / Zhang, S. / Sakuma, M. / Colletier, J.P. / Hay, S. / Schiro, G. / Weik, M. / Scrutton, N.S. / Leys, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c32.cif.gz | 340.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c32.ent.gz | 276.4 KB | Display | PDB format |
PDBx/mmJSON format | 8c32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/8c32 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/8c32 | HTTPS FTP |
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-Related structure data
Related structure data | 8c31SC 8c33C 8c34C 8c35C 8c36C 8c37C 8c73C 8c76C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23259.801 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_P0056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q746J7 #2: Chemical | ChemComp-BR / | #3: Chemical | ChemComp-B12 / #4: Chemical | ChemComp-5AD / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Condition B3 from Morpheus screen (Molecular Dimensions) (0.09 M halogens, 0.1 M buffer system 1 pH 6.5, 30% v/v precipitant mix 3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→57.4 Å / Num. obs: 46947 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 1 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2304 / CC1/2: 0.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8C31 Resolution: 2.2→57.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 13.433 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.629 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→57.39 Å
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Refine LS restraints |
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